{ "_id": "6abe3fea99f7aa8c6aa544c8", "Package": "MIML", "Type": "Package", "Title": "Machine Learning Imputation, Clustering and Survival Analysis\nfor Longitudinal Proteomic Data", "Version": "0.1.0", "Authors@R": "c(\nperson(\"Neelesh\", \"Kumar\", email = \"neelesh2302@gmail.com\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Atanu\", \"Bhattacharjee\", role = \"aut\"),\nperson(c(\"Gajendra\", \"K.\"), \"Vishwakarma\", role = \"aut\"),\nperson(\"Tanmoy\", \"Majumdar\", role = \"aut\"))", "Description": "Imputes missing biomarker measurements in a wide\nlongitudinal serum panel with gradient-boosted decision trees,\ngroups the completed panel by Bayesian consensus clustering,\nand compares the resulting patient subgroups by Kaplan-Meier,\nlog-rank and Cox analysis. The imputation learner is described\nin Ke et al. (2017)\n\nand the clustering method in Lock and Dunson (2013)\n. Imputed values are\nconditional-mean predictions, so the procedure is a\nmachine-learning single imputation; the completions carry no\nbetween-imputation variance and must not be pooled by Rubin's\nrules. Two panels from Gene Expression Omnibus accession\n'GSE65622' are included, one for each survival endpoint.", "License": "GPL-3", "Encoding": "UTF-8", "Config/testthat/edition": "3", "LazyData": "true", "LazyDataCompression": "xz", "Config/roxygen2/version": "8.1.0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-01 11:04:53 UTC", "User": "root" }, "Author": "Neelesh Kumar [aut, cre], Atanu Bhattacharjee [aut], Gajendra\nK. Vishwakarma [aut], Tanmoy Majumdar [aut]", "Maintainer": "Neelesh Kumar ", "Repository": "https://neelesh2302-creator.r-universe.dev", "Date/Publication": "2026-09-30 13:54:55 UTC", "RemoteUrl": "https://github.com/cran/MIML", "RemoteRef": "HEAD", "RemoteSha": "9eb513f496b9081139542bf69d98ffdacb4b5c8f", "_user": "neelesh2302-creator", "_type": "src", "_file": "MIML_0.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/bfd72f5c3289fed2dc7f811e251b3443e0b026259d15fd3e1c409e6e4745c0d8", "_filesize": 1797719, "_sha256": "bfd72f5c3289fed2dc7f811e251b3443e0b026259d15fd3e1c409e6e4745c0d8", "_expires": "2027-01-09T11:11:37.000Z", "_created": "2026-10-01T11:04:53.000Z", "_published": "2026-10-01T11:11:38.920Z", "_jobs": [ { "job": 110339296715, "time": 157, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11156427465" }, { "job": 110339296768, "time": 149, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11156671457" }, { "job": 110339296781, 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RIIA", "Adiponectin / Acrp30", "AgRP", "ALCAM", "Angiogenin", "Angiopoietin-1", "Angiopoietin-2", "Angiopoietin-4", "Angiopoietin-like 1", "Angiopoietin-like 2", "Angiopoietin-like Factor", "Angiostatin", "APJ", "APRIL", "AR (Amphiregulin)", "Artemin", "Axl", "B7-1 /CD80", "BAFF R / TNFRSF13C", "BCMA / TNFRSF17", "BD-1", "BDNF", "beta-Catenin", "beta-Defensin 2", "beta-NGF", "BIK", "BLC / BCA-1 / CXCL13", "BMP-15", "BMP-2", "BMP-3", "BMP-3b / GDF-10", "BMP-4", "BMP-5", "BMP-6", "BMP-7", "BMP-8", "BMPR-IA / ALK-3", "BMPR-IB / ALK-6", "BMPR-II", "BTC", "Cardiotrophin-1 / CT-1", "CCL14 / HCC-1 / HCC-3", "CCL28 / VIC", "CCR1", "CCR2", "CCR3", "CCR4", "CCR5", "CCR6", "CCR7", "CCR8", "CCR9", "CD 163", "CD14", "CD27 / TNFRSF7", "CD30 / TNFRSF8", "CD30 Ligand / TNFSF8", "CD40 / TNFRSF5", "CD40 Ligand / TNFSF5 /CD154", "Cerberus 1", "Chem R23", "Chordin-Like 1", "Chordin-Like 2", "CLC", "CNTF", "CNTF R alpha", "Coagulation Factor III / Tissue Factor", "CRIM 1", "Cripto-1", "CRTH-2", "Cryptic", 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"Frizzled-4", "Frizzled-5", "Frizzled-6", "Frizzled-7", "G-CSF R / CD 114", "Galectin-3", "GASP-1 / WFIKKNRP", "GASP-2 / WFIKKN", "GCP-2 / CXCL6", "GCSF", "GDF-15", "GDF1", "GDF11", "GDF3", "GDF5", "GDF8", "GDF9", "GDNF", "GFR alpha-1", "GFR alpha-2", "GFR alpha-3", "GFR alpha-4", "GITR / TNFRF18", "GITR Ligand / TNFSF18", "Glucagon", "Glut1", "Glut2", "Glut3", "Glut5", "Glypican 3", "Glypican 5", "GM-CSF", "GM-CSF R alpha", "Granzyme A", "GREMLIN", "GRO", "GRO-a", "Growth Hormone (GH)", "Growth Hormone R (GHR)", "HB-EGF", "HCC-4 / CCL16", "HCR / CRAM-A/B", "Hepassocin", "Heregulin / NDF / GGF", "HGF", "HGFR", "HRG-alpha", "HRG-beta 1", "HVEM / TNFRSF14", "I-309", "I-TAC / CXCL11", "ICAM-1", "ICAM-2", "ICAM-3 (CD50)", "ICAM-5", "IFN-alpha / beta R1", "IFN-alpha / beta R2", "IFN-beta", "IFN-gamma", "IFN-gamma R1", "IGF-I", "IGF-I SR", "IGF-II", "IGF-II R", "IGFBP-1", "IGFBP-2", "IGFBP-3", "IGFBP-4", "IGFBP-6", "IGFBP-rp1 / IGFBP-7", "IL-1 alpha", "IL-1 beta", "IL-1 F10 / IL-1HY2", "IL-1 F5 / FIL1delta", "IL-1 F6 / FIL1 epsilon", "IL-1 F7 / FIL1 zeta", "IL-1 F8 / FIL1 eta", "IL-1 F9 / IL-1 H1", "IL-1 R3 / IL-1 R AcP", "IL-1 R4 / ST2", "IL-1 R6 / IL-1 Rrp2", "IL-1 R8", "IL-1 R9", "IL-1 ra", "IL-1 sRI", "IL-1 sRII", "IL-10", "IL-10 R alpha", "IL-10 R beta", "IL-11", "IL-12 p40", "IL-12 p70", "IL-12 R beta 1", "IL-12 R beta 2", "IL-13", "IL-13 R alpha 1", "IL-13 R alpha 2", "IL-15", "IL-15 R alpha", "IL-16", "IL-17", "IL-17B", "IL-17B R", "IL-17C", "IL-17D", "IL-17E", "IL-17F", "IL-17R", "IL-17RC", "IL-17RD", "IL-18 BPa", "IL-18 R alpha /IL-1 R5", "IL-18 R beta /AcPL", "IL-19", "IL-2", "IL-2 R alpha", "IL-2 R beta /CD122", "IL-2 R gamma", "IL-20", "IL-20 R alpha", "IL-20 R beta", "IL-21", "IL-21 R", "IL-22", "IL-22 BP", "IL-22 R", "IL-23", "IL-23 R", "IL-24", "IL-26", "IL-27", "IL-28A", "IL-29", "IL-3", "IL-3 R alpha", "IL-31", "IL-31 RA", "IL-4", "IL-4 R", "IL-5", "IL-5 R alpha", "IL-6", "IL-6 R", "IL-7", "IL-7 R alpha", "IL-8", "IL-9", "Inhibin A", "Inhibin B", "Insulin", "Insulin R", "Insulysin / IDE", "IP-10", "Kininostatin / kininogen", "Kremen-1", "Kremen-2", "L-Selectin (CD62L)", "Latent TGF-beta bp1", "LBP", "Lck", "LECT2", "Lefty -A", "Leptin (OB)", "Leptin R", "LFA-1 alpha", "LIF", "LIF R alpha", "LIGHT / TNFSF14", "Lipocalin-1", "Lipocalin-2", "LRP-1", "LRP-6", "Lymphotactin / XCL1", "Lymphotoxin beta / TNFSF3", "Lymphotoxin beta R / TNFRSF3", "M-CSF", "M-CSF R", "MAC-1", "MCP-1", "MCP-2", "MCP-3", "MCP-4 / CCL13", "MDC", "MFG-E8", "MFRP", "MICA", "MIF", "MIG", "MIP 2", "MIP-1a", "MIP-1b", "MIP-1d", "MIP-3 alpha", "MIP-3 beta", "MMP-1", "MMP-10", "MMP-11 /Stromelysin-3", "MMP-12", "MMP-13", "MMP-14", "MMP-15", "MMP-16 / MT3-MMP", "MMP-19", "MMP-2", "MMP-20", "MMP-24 / MT5-MMP", "MMP-25 / MT6-MMP", "MMP-3", "MMP-7", "MMP-8", "MMP-9", "MSP alpha Chain", "Musk", "NAP-2", "NCAM-1 / CD56", "Neuritin", "NeuroD1", "Neuropilin-2", "Neurturin", "NGF R", "Nidgen-1", "NOV / CCN3", "NrCAM", "NRG1 Isoform GGF2", "NRG2", "NRG3", "NT-3", "NT-4", "Orexin A", "Orexin B", "OSM", "Osteoactivin / GPNMB", "Osteocrin", "Osteoprotegerin / TNFRSF11B", "OX40 Ligand / TNFSF4", "P-selectin", "PARC / CCL18", "PD-ECGF", "PDGF R alpha", "PDGF R beta", "PDGF-AA", "PDGF-AB", "PDGF-BB", "PDGF-C", "PDGF-D", "PECAM-1 /CD31", "Pentraxin3 / TSG-14", "Persephin", "PF4 / CXCL4", "PlGF", "PLUNC", "Pref-1", "Progranulin", "Prolactin", "RAGE", "RANK / TNFRSF11A", "RANTES", "RELM beta", "RELT / TNFRSF19L", "ROBO4", "S100 A8/A9", "S100A10", "SAA", "SCF", "SCF R /CD117", "SDF-1 / CXCL12", "sFRP-1", "sFRP-3", "sFRP-4", "sgp130", "SIGIRR", "Siglec-5/CD170", "Siglec-9", "SLPI", "Smad 1", "Smad 4", "Smad 5", "Smad 7", "Smad 8", "SMDF / NRG1Isoform", "Soggy-1", "Sonic Hedgehog (Shh N-terminal)", "SPARC", "Spinesin", "TACI / TNFRSF13B", "Tarc", "TCCR / WSX-1", "TECK / CCL25", "TFPI", "TGF-alpha", "TGF-beta 1", "TGF-beta 2", "TGF-beta 3", "TGF-beta 5", "TGF-beta RI / ALK-5", "TGF-beta RII", "TGF-beta RIIb", "TGF-beta RIII", "Thrombopoietin (TPO)", "Thrombospondin (TSP)", "Thrombospondin-1", "Thrombospondin-2", "Thrombospondin-4", "Thymopoietin", "Tie-1", "Tie-2", "TIMP-1", "TIMP-2", "TIMP-3", "TIMP-4", "TL1A / TNFSF15", "TLR1", "TLR2", "TLR3", "TLR4", "TMEFF1 / Tomoregulin-1", "TMEFF2", "TNF RI / TNFRSF1A", "TNF RII / TNFRSF1B", "TNF-alpha", "TNF-beta", "TRADD", "TRAIL / TNFSF10", "TRAIL R1 / DR4 / TNFRSF10A", "TRAIL R2 / DR5 / TNFRSF10B", "TRAIL R3 / TNFRSF10C", "TRAIL R4 / TNFRSF10D", "TRANCE", "TREM-1", "TROY / TNFRSF19", "TSG-6", "TSLP R", "TWEAK / TNFSF12", "TWEAK R / TNFRSF12", "Ubiquitin+1", "uPA", "uPAR", "Vasorin", "VCAM-1 (CD106)", "VE-Cadherin", "VEGF", "VEGF R2 (KDR)", "VEGF R3", "VEGF-B", "VEGF-C", "VEGF-D", "VEGI / TNFSF15", "WIF-1", "WISP-1 / CCN4", "XEDAR", "diarrhea_grade", "sampling_point", "slide_print_batch", "trg_score", "ypn_stage", "ypt_stage" ], "rows": 288, "table": true, "tojson": true }, { "name": "RFS_data", "title": "Recurrence-free survival panel (GSE65622)", "object": "RFS_data", "class": [ "data.frame" ], "fields": [ "Patient_ID", "RFS", "event", "6Ckine", "Activin A", "Activin B", "Activin C", "Activin RIA / ALK-2", "Activin RIB / ALK-4", "Activin RII A/B", "Activin RIIA", "Adiponectin / Acrp30", "AgRP", "ALCAM", "Angiogenin", "Angiopoietin-1", "Angiopoietin-2", "Angiopoietin-4", "Angiopoietin-like 1", "Angiopoietin-like 2", "Angiopoietin-like Factor", "Angiostatin", "APJ", "APRIL", "AR (Amphiregulin)", "Artemin", "Axl", "B7-1 /CD80", "BAFF R / TNFRSF13C", "BCMA / TNFRSF17", "BD-1", "BDNF", "beta-Catenin", "beta-Defensin 2", "beta-NGF", "BIK", "BLC / BCA-1 / CXCL13", "BMP-15", "BMP-2", "BMP-3", "BMP-3b / GDF-10", "BMP-4", "BMP-5", "BMP-6", "BMP-7", "BMP-8", "BMPR-IA / ALK-3", "BMPR-IB / ALK-6", "BMPR-II", "BTC", "Cardiotrophin-1 / CT-1", "CCL14 / HCC-1 / HCC-3", "CCL28 / VIC", "CCR1", "CCR2", "CCR3", "CCR4", "CCR5", "CCR6", "CCR7", "CCR8", "CCR9", "CD 163", "CD14", "CD27 / TNFRSF7", "CD30 / TNFRSF8", "CD30 Ligand / TNFSF8", "CD40 / TNFRSF5", "CD40 Ligand / TNFSF5 /CD154", "Cerberus 1", "Chem R23", "Chordin-Like 1", "Chordin-Like 2", "CLC", "CNTF", "CNTF R alpha", "Coagulation Factor III / Tissue Factor", "CRIM 1", "Cripto-1", "CRTH-2", "Cryptic", "Csk", "CTACK / CCL27", "CTGF / CCN2", "CTLA-4 /CD152", "CV-2 / Crossveinless-2", "CXCL14 / BRAK", "CXCL16", "CXCR1 / IL-8 RA", "CXCR2 / IL-8 RB", "CXCR3", "CXCR4 (fusin)", "CXCR5 /BLR-1", "CXCR6", "D6", "DAN", "DANCE", "DcR3 / TNFRSF6B", "Decorin", "Dkk-1", "Dkk-3", "Dkk-4", "DR3 / TNFRSF25", "DR6 / TNFRSF21", "Dtk", "E-Selectin", "EDA-A2", "EDAR", "EDG-1", "EG-VEGF / PK1", "EGF", "EGF R / ErbB1", "EMAP-II", "EN-RAGE", "ENA-78", "Endocan", "Endoglin / CD105", "Endostatin", "Endothelin", "Eotaxin / CCL11", "Eotaxin-2 / MPIF-2", "Eotaxin-3 / CCL26", "Epiregulin", "ErbB2", "ErbB3", "ErbB4", "Erythropoietin", "FADD", "FAM3B", "Fas / TNFRSF6", "Fas Ligand", "FGF Basic", "FGF R3", "FGF R4", "FGF R5", "FGF-10 / KGF-2", "FGF-11", "FGF-12", "FGF-13 1B", "FGF-16", "FGF-17", "FGF-18", "FGF-19", "FGF-20", "FGF-21", "FGF-23", "FGF-4", "FGF-5", "FGF-6", "FGF-7 / KGF", "FGF-8", "FGF-9", "FGF-BP", "FLRG", "Flt-3 Ligand", "Follistatin", "Follistatin-like 1", "Fractalkine", "Frizzled-1", "Frizzled-3", "Frizzled-4", "Frizzled-5", "Frizzled-6", "Frizzled-7", "G-CSF R / CD 114", "Galectin-3", "GASP-1 / WFIKKNRP", "GASP-2 / WFIKKN", "GCP-2 / CXCL6", "GCSF", "GDF-15", "GDF1", "GDF11", "GDF3", "GDF5", "GDF8", "GDF9", "GDNF", "GFR alpha-1", "GFR alpha-2", "GFR alpha-3", "GFR alpha-4", "GITR / TNFRF18", "GITR Ligand / TNFSF18", "Glucagon", "Glut1", "Glut2", "Glut3", "Glut5", "Glypican 3", "Glypican 5", "GM-CSF", "GM-CSF R alpha", "Granzyme A", "GREMLIN", "GRO", "GRO-a", "Growth Hormone (GH)", "Growth Hormone R (GHR)", "HB-EGF", "HCC-4 / CCL16", "HCR / CRAM-A/B", "Hepassocin", "Heregulin / NDF / GGF", "HGF", "HGFR", "HRG-alpha", "HRG-beta 1", "HVEM / TNFRSF14", "I-309", "I-TAC / CXCL11", "ICAM-1", "ICAM-2", "ICAM-3 (CD50)", "ICAM-5", "IFN-alpha / beta R1", "IFN-alpha / beta R2", "IFN-beta", "IFN-gamma", "IFN-gamma R1", "IGF-I", "IGF-I SR", "IGF-II", "IGF-II R", "IGFBP-1", "IGFBP-2", "IGFBP-3", "IGFBP-4", "IGFBP-6", "IGFBP-rp1 / IGFBP-7", "IL-1 alpha", "IL-1 beta", "IL-1 F10 / IL-1HY2", "IL-1 F5 / FIL1delta", "IL-1 F6 / FIL1 epsilon", "IL-1 F7 / FIL1 zeta", "IL-1 F8 / FIL1 eta", "IL-1 F9 / IL-1 H1", "IL-1 R3 / IL-1 R AcP", "IL-1 R4 / ST2", "IL-1 R6 / IL-1 Rrp2", "IL-1 R8", "IL-1 R9", "IL-1 ra", "IL-1 sRI", "IL-1 sRII", "IL-10", "IL-10 R alpha", "IL-10 R beta", "IL-11", "IL-12 p40", "IL-12 p70", "IL-12 R beta 1", "IL-12 R beta 2", "IL-13", "IL-13 R alpha 1", "IL-13 R alpha 2", "IL-15", "IL-15 R alpha", "IL-16", "IL-17", "IL-17B", "IL-17B R", "IL-17C", "IL-17D", "IL-17E", "IL-17F", "IL-17R", "IL-17RC", "IL-17RD", "IL-18 BPa", "IL-18 R alpha /IL-1 R5", "IL-18 R beta /AcPL", "IL-19", "IL-2", "IL-2 R alpha", "IL-2 R beta /CD122", "IL-2 R gamma", "IL-20", "IL-20 R alpha", "IL-20 R beta", "IL-21", "IL-21 R", "IL-22", "IL-22 BP", "IL-22 R", "IL-23", "IL-23 R", "IL-24", "IL-26", "IL-27", "IL-28A", "IL-29", "IL-3", "IL-3 R alpha", "IL-31", "IL-31 RA", "IL-4", "IL-4 R", "IL-5", "IL-5 R alpha", "IL-6", "IL-6 R", "IL-7", "IL-7 R alpha", "IL-8", "IL-9", "Inhibin A", "Inhibin B", "Insulin", "Insulin R", "Insulysin / IDE", "IP-10", "Kininostatin / kininogen", "Kremen-1", "Kremen-2", "L-Selectin (CD62L)", "Latent TGF-beta bp1", "LBP", "Lck", "LECT2", "Lefty -A", "Leptin (OB)", "Leptin R", "LFA-1 alpha", "LIF", "LIF R alpha", "LIGHT / TNFSF14", "Lipocalin-1", "Lipocalin-2", "LRP-1", "LRP-6", "Lymphotactin / XCL1", "Lymphotoxin beta / TNFSF3", "Lymphotoxin beta R / TNFRSF3", "M-CSF", "M-CSF R", "MAC-1", "MCP-1", "MCP-2", "MCP-3", "MCP-4 / CCL13", "MDC", "MFG-E8", "MFRP", "MICA", "MIF", "MIG", "MIP 2", "MIP-1a", "MIP-1b", "MIP-1d", "MIP-3 alpha", "MIP-3 beta", "MMP-1", "MMP-10", "MMP-11 /Stromelysin-3", "MMP-12", "MMP-13", "MMP-14", "MMP-15", "MMP-16 / MT3-MMP", "MMP-19", "MMP-2", "MMP-20", "MMP-24 / MT5-MMP", "MMP-25 / MT6-MMP", "MMP-3", "MMP-7", "MMP-8", "MMP-9", "MSP alpha Chain", "Musk", "NAP-2", "NCAM-1 / CD56", "Neuritin", "NeuroD1", "Neuropilin-2", "Neurturin", "NGF R", "Nidgen-1", "NOV / CCN3", "NrCAM", "NRG1 Isoform GGF2", "NRG2", "NRG3", "NT-3", "NT-4", "Orexin A", "Orexin B", "OSM", "Osteoactivin / GPNMB", "Osteocrin", "Osteoprotegerin / TNFRSF11B", "OX40 Ligand / TNFSF4", "P-selectin", "PARC / CCL18", "PD-ECGF", "PDGF R alpha", "PDGF R beta", "PDGF-AA", "PDGF-AB", "PDGF-BB", "PDGF-C", "PDGF-D", "PECAM-1 /CD31", "Pentraxin3 / TSG-14", "Persephin", "PF4 / CXCL4", "PlGF", "PLUNC", "Pref-1", "Progranulin", "Prolactin", "RAGE", "RANK / TNFRSF11A", "RANTES", "RELM beta", "RELT / TNFRSF19L", "ROBO4", "S100 A8/A9", "S100A10", "SAA", "SCF", "SCF R /CD117", "SDF-1 / CXCL12", "sFRP-1", "sFRP-3", "sFRP-4", "sgp130", "SIGIRR", "Siglec-5/CD170", "Siglec-9", "SLPI", "Smad 1", "Smad 4", "Smad 5", "Smad 7", "Smad 8", "SMDF / NRG1Isoform", "Soggy-1", "Sonic Hedgehog (Shh N-terminal)", "SPARC", "Spinesin", "TACI / TNFRSF13B", "Tarc", "TCCR / WSX-1", "TECK / CCL25", "TFPI", "TGF-alpha", 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